If you have a Mac that has been rebuilt because it was infected with the Flashback Trojan, and you want to restore your files using Time Machine, restore ONLY the user profiles and applications. DO NOT restore system files or library files – they can re-infect your Mac with malware, which will result in your Mac being quarantined again.
If you use another backup tool for your Mac, use caution when restoring anything other than your data files; you may re-introduce the infection to your Mac. Check the vendor's information for help on backups and restores.